Abstract
This report summarizes the output of population genetic analyses of a
pool-seq RAD library.
Filtering
Stepwise filtering reuslts
SNPs remaining after each filtering step.
Note: filtering results displayed are independent, not
cumulative.
Filter options with no effect: max_missing, min_mean_depth,
min_pools.
Cumulative filtering results
SNPs remaining after each filtering step.
Cumulative filter results
(Note: filtered SNP count may differ
from SNP counts associated with Fst calculations).
High-level summaries
grenedalf
All SNPs
Plot
Global summary statistics by coverage cutoff
Table
Global summary statistics by coverage cutoff
SNPs shared by all pools
Plot
Global summary statistics by coverage cutoff
Table
Global summary statistics by coverage cutoff
poolfstat
All SNPs
Plot
Global summary statistics by coverage cutoff
Table
Global summary statistics by coverage cutoff
SNPs shared by all pools
Plot
Global summary statistics by coverage cutoff
Table
Global summary statistics by coverage cutoff
popoolation
All SNPs
Plot
Global summary statistics by coverage cutoff
Table
Global summary statistics by coverage cutoff
SNPs shared by all pools
Plot
Global summary statistics by coverage cutoff
Table
Global summary statistics by coverage cutoff
Pairwise Fst by minimum coverage
grenedalf
All SNPs
Box plot (distributions)
Note: subsampled to 30 outliers per pair.
SNPs shared by all pools
Box plot (distributions)
Note: subsampled to 30 outliers per pair.
poolfstat
All SNPs
Box plot (distributions)
Note: subsampled to 30 outliers per pair.
SNPs shared by all pools
Box plot (distributions)
Note: subsampled to 30 outliers per pair.
popoolation
All SNPs
Box plot (distributions)
Note: subsampled to 30 outliers per pair.
SNPs shared by all pools
Box plot (distributions)
Note: subsampled to 30 outliers per pair.
Summary statistic heatmaps
grenedalf
All SNPs
Fst (±SD)
Lower triangle: mean pairwise Fst
Upper triangle: standard
deviation of Fst
Note: Grey cells indicate missing data.
SNPs / SNPs per contig
Lower triangle: pairwise shared SNPs contributing to Fst
calculation
Upper triangle: average shared SNPs per contig
Note: Grey cells indicate missing data.
Mean coverage (±SD)
Lower triangle: mean pairwise coverage
Upper triangle: pairwise
coverage standard deviation
Note: Grey cells indicate missing data.
Contigs
Pairwise shared contigs
Note: Grey cells indicate missing data.
SNPs shared by all pools
Fst (±SD)
Lower triangle: mean pairwise Fst
Upper triangle: standard
deviation of Fst
Note: Grey cells indicate missing data.
SNPs / SNPs per contig
Lower triangle: pairwise shared SNPs contributing to Fst
calculation
Upper triangle: average shared SNPs per contig
Note: Grey cells indicate missing data.
Mean coverage (±SD)
Lower triangle: mean pairwise coverage
Upper triangle: pairwise
coverage standard deviation
Note: Grey cells indicate missing data.
Contigs
Pairwise shared contigs
Note: Grey cells indicate missing data.
poolfstat
All SNPs
Fst (±SD)
Lower triangle: mean pairwise Fst
Upper triangle: standard
deviation of Fst
Note: Grey cells indicate missing data.
SNPs / SNPs per contig
Lower triangle: pairwise shared SNPs contributing to Fst
calculation
Upper triangle: average shared SNPs per contig
Note: Grey cells indicate missing data.
Mean coverage (±SD)
Lower triangle: mean pairwise coverage
Upper triangle: pairwise
coverage standard deviation
Note: Grey cells indicate missing data.
Contigs
Pairwise shared contigs
Note: Grey cells indicate missing data.
SNPs shared by all pools
Fst (±SD)
Lower triangle: mean pairwise Fst
Upper triangle: standard
deviation of Fst
Note: Grey cells indicate missing data.
SNPs / SNPs per contig
Lower triangle: pairwise shared SNPs contributing to Fst
calculation
Upper triangle: average shared SNPs per contig
Note: Grey cells indicate missing data.
Mean coverage (±SD)
Lower triangle: mean pairwise coverage
Upper triangle: pairwise
coverage standard deviation
Note: Grey cells indicate missing data.
Contigs
Pairwise shared contigs
Note: Grey cells indicate missing data.
popoolation
All SNPs
Fst (±SD)
Lower triangle: mean pairwise Fst
Upper triangle: standard
deviation of Fst
Note: Grey cells indicate missing data.
SNPs / SNPs per contig
Lower triangle: pairwise shared SNPs contributing to Fst
calculation
Upper triangle: average shared SNPs per contig
Note: Grey cells indicate missing data.
Mean coverage (±SD)
Lower triangle: mean pairwise coverage
Upper triangle: pairwise
coverage standard deviation
Note: Grey cells indicate missing data.
Contigs
Pairwise shared contigs
Note: Grey cells indicate missing data.
SNPs shared by all pools
Fst (±SD)
Lower triangle: mean pairwise Fst
Upper triangle: standard
deviation of Fst
Note: Grey cells indicate missing data.
SNPs / SNPs per contig
Lower triangle: pairwise shared SNPs contributing to Fst
calculation
Upper triangle: average shared SNPs per contig
Note: Grey cells indicate missing data.
Mean coverage (±SD)
Lower triangle: mean pairwise coverage
Upper triangle: pairwise
coverage standard deviation
Note: Grey cells indicate missing data.
Contigs
Pairwise shared contigs
Note: Grey cells indicate missing data.
Fst method correlations
grenedalf vs poolfstat
Note: Due to potentially large datasets, only a subsample of
1,000 Fst values is shown here.
grenedalf vs popoolation
Note: Due to potentially large datasets, only a subsample of
1,000 Fst values is shown here.
poolfstat vs popoolation
Note: Due to potentially large datasets, only a subsample of
1,000 Fst values is shown here.
Fisher’s test plots
Fisher test results are presented as static plots since these
datasets can get huge, making plotly go slow or crash.
assesspool
Points above red line indicate p < 0.05.
popoolation
Points above red line indicate p < 0.05.